musaline::Alignment Struct Reference

#include <musaline.hpp>

Public Attributes
double	score
	The computed similarity value for the alignment.
size_t	start [2]
	start[i] points to the start of the matched part of sequence i. More...
size_t	end [2]
	end[i] points one after the end of the matched part of sequence i.
std::vector< Match >	matches
	This vector holds details of the parts of seq0 and seq1 that are matched with each other.

Detailed Description

An Alignment records how two sequences (seq0 and seq1) are aligned.

Some invariants hold between the matches and the other values.

• The score is the sum of all matches[i].score
• end[j]-start[j] is the sum of all matches[i].n[j], for j equal to 0 or 1.

Member Data Documentation

size_t musaline::Alignment::start[2]

start[i] points to the start of the matched part of sequence i.

start[i] together with end[i] indicates the subsequence that was matched of sequence i. start indicates the first element. start[i]<=end[i], and end[i]-start[i] is the length of the subsequence that is matched.

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The documentation for this struct was generated from the following file:

• include/musaline.hpp